get_sig_rec_similarity

See bp_extract_signatures for examples.

Genomic alterations including single nucleotide substitution,
copy number alteration, etc. are the major force for cancer
initialization and development. Due to the specificity of molecular
lesions caused by genomic alterations, we can generate characteristic
alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021)
<DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al.
(2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al.
(2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to
extract, analyze and visualize signatures from genomic alteration
records, thus providing new insight into cancer study.

Shixiang Wang

sigminer

Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations

Ziyu Tao

Huimin Li

Tao Wu

Xue-Song Liu

Anand Mayakonda

get_sig_rec_similarity function

<dl><dt>Signature</dt>
<dd>a <code>Signature</code> object.</dd>
<dt>nmf_matrix</dt>
<dd>a <code>matrix</code> used for NMF decomposition with rows indicate samples and columns indicate components.</dd></dl>

Arguments

Get Reconstructed Profile Cosine Similarity, RSS, etc. — get_sig_rec_similarity

<dl>

<dt>Signature</dt>
<dd>a <code>Signature</code> object.</dd>


<dt>nmf_matrix</dt>
<dd>a <code>matrix</code> used for NMF decomposition with rows indicate samples and columns indicate components.</dd>

</dl>

get_sig_rec_similarity: Get Reconstructed Profile Cosine Similarity, RSS, etc.

Description

Usage

Value

Arguments